Solutions of exercises through part 4.

docs/programmers/tutorials/workflows/solutions/ex2a.py

@@ -6,7 +6,7 @@
 from gc3libs.cmdline import SessionBasedScript
 
 if __name__ == '__main__':
-    from day1 import AScript
+    from ex2a import AScript
     AScript().run()
 
 class AScript(SessionBasedScript):

docs/programmers/tutorials/workflows/solutions/ex2b.py

@@ -9,33 +9,22 @@
 
 
 if __name__ == '__main__':
-    from ex2b import AScript
-    AScript().run()
+    from ex2b import GrayscalingScript
+    GrayscalingScript().run()
 
 
-class AScript(SessionBasedScript):
+# alternatively, you can just copy+paste
+# the code for `GrayscaleApp` here
+from grayscale_app import GrayscaleApp
+
+
+class GrayscalingScript(SessionBasedScript):
     """
-    Minimal workflow scaffolding.
+    Convert an image to grayscale.
     """
     def __init__(self):
-        super(AScript, self).__init__(version='1.0')
+        super(GrayscalingScript, self).__init__(version='1.0')
     def new_tasks(self, extra):
         input_file = abspath(self.params.args[0])
-        app = GrayscaleApp(input_file)
-        return [app]
-
-
-class GrayscaleApp(Application):
-    """Convert a single image file to grayscale."""
-    def __init__(self, img):
-        inp = basename(img)
-        out = "gray-" + inp
-        Application.__init__(
-            self,
-            arguments=[
-                "convert", inp, "-colorspace", "gray", out],
-            inputs=[img],
-            outputs=[out],
-            output_dir="grayscale.d",
-            stdout="stdout.txt",
-            stderr="stderr.txt")
+        apps_to_run = [ GrayscaleApp(input_file) ]
+        return apps_to_run

docs/programmers/tutorials/workflows/solutions/ex2c.py

@@ -10,16 +10,16 @@
 
 
 if __name__ == '__main__':
-    from ex2c import AScript
-    AScript().run()
+    from ex2c import GrayscaleScript
+    GrayscaleScript().run()
 
 
-class AScript(SessionBasedScript):
+class GrayscaleScript(SessionBasedScript):
     """
-    Minimal workflow scaffolding.
+    Convert images to grayscale.
     """
     def __init__(self):
-        super(AScript, self).__init__(version='1.0')
+        super(GrayscaleScript, self).__init__(version='1.0')
     def new_tasks(self, extra):
         # since `self.params.args` is already a list of file names,
         # just iterate over it to build the list of apps to run...
@@ -30,6 +30,8 @@ def new_tasks(self, extra):
         return apps_to_run
 
 
+# alternatively, you could use
+# `from grayscale_app import GrayscaleApp` above
 class GrayscaleApp(Application):
     """Convert a single image file to grayscale."""
     def __init__(self, img):
@@ -41,6 +43,9 @@ def __init__(self, img):
                 "convert", inp, "-colorspace", "gray", out],
             inputs=[img],
             outputs=[out],
+            # need to use a different output dir per set of
+            # construction params, otherwise the output of one task
+            # will be overwritten by another task's output ...
             output_dir=("gray-" + inp + ".d"),
             stdout="stdout.txt",
             stderr="stderr.txt",

docs/programmers/tutorials/workflows/solutions/ex4a.py

@@ -0,0 +1,56 @@
+#! /usr/bin/env python
+
+import os
+from os.path import abspath, basename
+import sys
+
+from gc3libs import Application
+from gc3libs.cmdline import SessionBasedScript
+
+
+if __name__ == '__main__':
+    from ex4a import ColorizeScript
+    ColorizeScript().run()
+
+
+class ColorizeScript(SessionBasedScript):
+    """
+    Coloriye multiple images.
+    """
+    def __init__(self):
+        super(ColorizeScript, self).__init__(version='1.0')
+    def setup_args(self):
+        self.add_param('colors', nargs=3,   help="Three colors")
+        self.add_param('images', nargs='+', help="Images to colorize")
+    def new_tasks(self, extra):
+        col1, col2, col3 = self.params.colors
+        apps_to_run = []
+        for input_file in self.params.images:
+            input_file = abspath(input_file)
+            apps_to_run.append(ColorizeApp(input_file, col1, col2, col3))
+        return apps_to_run
+
+
+from gc3libs.quantity import GB
+
+class ColorizeApp(Application):
+    """Add colors to a grayscale image."""
+    def __init__(self, img, col1, col2, col3):
+        inp = basename(img)
+        out = "color-" + inp
+        Application.__init__(
+            self,
+            arguments=[
+                "convert", inp,
+                "(", "xc:"+col1,  "xc:"+col2, "xc:"+col3, "+append", ")", "-clut",
+                out],
+            inputs=[img],
+            outputs=[out],
+            # need to use a different output dir per set of
+            # construction params, otherwise the output of one task
+            # will be overwritten by another task's output ...
+            output_dir="colorized-" + inp + ".d",
+            stdout="stdout.txt",
+            stderr="stderr.txt",
+            # required for running on the cloud, see GC3Pie issue #559
+            requested_memory=1*GB)

docs/programmers/tutorials/workflows/solutions/ex4b.py

@@ -0,0 +1,58 @@
+#! /usr/bin/env python
+
+import os
+from os.path import abspath, basename
+import sys
+
+from gc3libs import Application
+from gc3libs.cmdline import SessionBasedScript
+
+
+if __name__ == '__main__':
+    from ex4b import TopBlastScript
+    TopBlastScript().run()
+
+
+class TopBlastScript(SessionBasedScript):
+    """
+    Run BLAST on pairs of FAA files.
+    """
+    def __init__(self):
+        super(TopBlastScript, self).__init__(version='1.0')
+    def setup_args(self):
+        self.add_param('new_faa', help="Query FAA")
+        self.add_param('known_faa', nargs='+',
+                       help="Samples to compare to the query")
+    def setup_options(self):
+        self.add_param('--e-value', '-e',
+                       type=float, help="Expectation value")
+        self.add_param('--output-format', '-o', dest='output_fmt',
+                       type=int, help="Output format, int from 0 to 9")
+    def new_tasks(self, extra):
+        apps_to_run = []
+        for in_file2 in self.params.known_faa:
+            in_file2 = abspath(in_file2)
+            apps_to_run.append(BlastApp(self.params.new_faa, in_file2,
+                                        self.params.e_value, self.params.output_fmt))
+        return apps_to_run
+
+
+from gc3libs.quantity import GB
+
+class BlastApp(Application):
+    """Run BLAST on two files."""
+    def __init__(self, input1, input2, e_value, output_fmt):
+        inp1 = basename(input1)
+        inp2 = basename(input2)
+        Application.__init__(
+            self,
+            # NOTE: does not work as written! BLAST+ is required
+            # to compare two FASTA files
+            arguments=["blastpgp", "-i", inp1, "-d", inp2,
+                       "-e", e_value, "-m", output_fmt, "-o", "output.txt"],
+            inputs=[input1, input2],
+            outputs=["output.txt"],
+            output_dir=("blast-" + inp1 + "-" + inp2 + ".d"),
+            stdout="stdout.txt",
+            stderr="stderr.txt",
+            requested_memory=1*GB)